"""
Command line utility to generate output sections from
a CWL tool or sub-workflow.
Generated sections then can be copied and pasted into
any calling workflow
"""
# Copyright (c) 2021. Harvard University
#
# Developed by Research Software Engineering,
# Faculty of Arts and Sciences, Research Computing (FAS RC)
# Author: Michael A Bouzinier
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.
#
import os
import sys
from argparse import ArgumentParser
import yaml
[docs]def encode(name: str):
if len(name) < 13:
return name + '_'
else:
return name[:9] + str(hash(name) % 1000) + '_'
[docs]def collect(step: str, path: str, name = None, output = sys.stdout, what=None):
if what is None:
what = ["step", "pipeline"]
if name is None:
name = step
with open(path) as f:
cwl = yaml.safe_load(f)
outputs = cwl["outputs"]
if "step" in what:
print(" out:", file=output)
for o in outputs:
t = outputs[o]["type"]
print(" - {}".format(o), file=output)
if "pipeline" in what:
print("## Generated by nsaph/util/cwl_collect_outputs.py from {}:".
format(os.path.basename(path)), file=output)
for o in outputs:
t = outputs[o]["type"]
if isinstance(t, str) and t.lower() in ["stdout", "stderr"]:
t = "File"
print(" {}:".format(encode(name) + o), file=output)
print(" type: {}".format(t), file=output)
print(" outputSource: {}/{}".format(step, o), file=output)
[docs]def parse_args():
parser = ArgumentParser (
description="Collect outputs from CWL sub-workflow and print"
"outputs section to be added for enveloping workflow"
)
parser.add_argument(
dest="step",
help="Step name in the outer (calling) workflow"
)
parser.add_argument(
dest = "path",
help="Path to sub-workflow CWL file"
)
parser.add_argument(
"--name",
help="Name to be used as output prefix, defaults to the step name",
required=False
)
return parser.parse_args()
if __name__ == '__main__':
arguments = parse_args()
collect(arguments.step, arguments.path, arguments.name)